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Molecular Modelling

Code: Q345     Acronym: Q345

Classification Keyword
OFICIAL Chemistry

Instance: 2013/2014 - 1S Ícone do Moodle

Active? Yes
Web Page: http://elearning2.fc.up.pt/aulasweb/course/view.php?id=3488
Responsible unit: Department of Chemistry and Biochemistry
Course/CS Responsible: Bachelor in Chemistry

Cycles of Study/Courses

Acronym No. of Students Study Plan Curricular Years Credits UCN Credits ECTS Contact hours Total Time
L:Q 33 Plano de estudos Oficial 3 - 5 56 135

Teaching Staff - Responsibilities

Teacher Responsibility
Maria Natália Dias Soeiro Cordeiro
Alexandre Lopes de Magalhães

Teaching - Hours

Theoretical and practical : 2,00
Laboratory Practice: 2,00
Type Teacher Classes Hour
Theoretical and practical Totals 1 2,00
Alexandre Lopes de Magalhães 1,00
Maria Natália Dias Soeiro Cordeiro 1,00
Laboratory Practice Totals 2 4,00
Alexandre Lopes de Magalhães 2,00
Maria Natália Dias Soeiro Cordeiro 2,00

Teaching language



Application of theoretical models to predict and interpret physical and chemical properties of simple molecular systems. Familiarity with computer programs for calculation, visualization and manipulation of molecular models in Linux operating system.

Learning outcomes and competences

On successful completion of this course the student will be able to:

- Distinguish classical and quantum modeling methods, concerning their applicability, data type of input and output.

- Run and interpret the results of Hartree-Fock(HF) quantum calculations using the Gaussian09 program.

- Apply HF calculations to study the geometric stability of molecules, and the mechanism of a simple chemical reaction.

- Run and interpret the results of molecular dynamics(MD) simulations using the program Gromacs.

- Apply MD simulations to study the hydration of monoatomic ions.

Working method



This course is structured into three modules that correspond to three distinct computing works, including: I-Quantum calculation of molecular properties (Hartree-Fock) II-Modeling a chemical reaction of the SN2 type (Hartree-Fock) III-Study of solvated system (Molecular Dynamics method) Theory behind the calculation methods used (quantum and classical methods, respectively, Hartree-Fock and Molecular Dynamics). Using the Gaussian03 program package and the GROMACS molecular dynamics program. Using programs for visualization and manipulation of molecular models, GaussView and Molden.

Mandatory literature

Hinchliffe Alan; Molecular Modelling for beginners, Wiley, 2008
C. J. Cramer; Essentials of Computational Chemistry: Theories and Models , John Wiley & Sons Ltd, 2002
A. R. Leach; Molecular Modelling-Principles and Applications, Prentice Hall, 2001
F. Jensen; Introduction to Computational Chemistry, John Wiley & Sons , 1999
F. M. S. S. Fernandes; Cinquentenário da Simulação Computacional em Mecânica Estatística, Bol. Soc. Port. Química, vol. 93, pag. 49, 2004

Teaching methods and learning activities

Modern techniques of molecular modeling are discussed in this course. Each classroom has a maximum of 20 students which are organized in working groups of two elements. Classes are held in a dedicated room equipped with 20 computers Dual / intel on Linux environment and connected to the Internet; a projector and a blackboard are also available. Learning takes place according to a PBL (problem-based learning) paradigm in which students are confronted with a series of problems over the implementation of three projects whose resolution requires the knowledge of the underlying theoretical foundations. The teacher will moderate discussions between the working groups and, whenever necessary for the development of projects, he will give a brief explanation or demonstration in the laboratory. Although all the groups have to perform the three practical works, one of them will be attributed randomly to each group for final oral presentation. Those presentations will take place in the last class of the semester and will have a maximum duration of 15 minutes. They are followed by a short period of discussion with the audience, and each group will evaluate them using a five grade scale.


Gaussian09; Gaussview04; Molden; VMD; Grace


Physical sciences > Chemistry > Computational chemistry

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation Weight (%)
Prova oral 50,00
Exame 50,00
Total: 100,00

Eligibility for exams

The maximum number of absences allowed is 25% of the total number of planned classes, as determined by the existing rule in this Faculty. All normal students who completed at least 2 in 3 computer projects can be proposed to exam worth 50% of the final grade.

Calculation formula of final grade

Oral presentation - 50% of final grade Exam - 50% of final grade (Minimum rating required in the exam is 7/20)

Examinations or Special Assignments


Special assessment (TE, DA, ...)

Working students and association leaders may opt for a practical assessment alternative that consists of making a practical work to be randomly selected among those held during the semester and then elaborate its report.

Classification improvement

The improvement of the final classification can be done by repeating the exam component, worth 50% of the final grade, made in the appropriate exam season. The note will be corrected only if the new calculation of the note leads to a higher value. If a student wishes to improve the rating in the following academic year, it will have to do the exam component. It is not possible to improve the grade of the practical component.

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